[gmx-users] grompp fatal error Unknown bond_atomtype

chris.neale at utoronto.ca chris.neale at utoronto.ca
Wed Jun 23 05:00:25 CEST 2010

There's lots of information in the gromacs manual to show that the  
.atp file is not the only file that you must modify. My most important  
suggestion to you is that you should read the entire manual, possibly  
twice, before attempting to build new molecules.

Gromacs manual, page 96:
5.3.1    Atoms
A number of static properties are assigned to the atom types in the  
GROMACS force field: Type, Mass, Charge, and ? (see Table 5.2 The mass  
is listed in ff???.atp (see 5.2.1), whereas the charge is listed in  
ff???.rtp (.rtp = residue topology parameter file, see 5.6.1). This  
implies that the charges are only defined in the building blocks of  
amino acids or user defined building blocks. When generating a  
topology (*.top) using the pdb2gmx program the information from these  
files is combined.

Then on page 97:
"In the file ff???bon.itp you can add bonded parameters. If you want  
to include parameters for new atom types, make sure you define this  
new atom type in ff???.atp as well."

Then on page 120:
For each force field there a five files which are only used by  
pdb2gmx. These are: the residue database (.rtp, see 5.6.1) the  
hydrogen database (.hdb, see 5.6.2), two termini databases (.tdb, see  
5.6.3) and the atom type database (.atp) which contains only the masses.

I'm not going to post a detailed account of how to add an atom because  
it is key for you to fully understand what all of the forcefield files  
are doing if you are going to do something like create a new atom  
type. The information is all in the manual though, and search "exotic  
species" on the wiki, although lots of links there are still broken  
after the migration to a new wiki type.

By the way, you didn't post nearly enough information! You are trying  
to parameterize a new molecule and you got an error and the only thing  
that you posted was the error message ..... you're much more likely to  
get good help if you make it easier for everybody else to help you.


-- original message --

Hi Users,

I am experiencing the following fatal error when I try using the
grompp command.

grompp -f mdout.mdp -r conf.gro -p topol.top

Program grompp, VERSION 4.0.99-dev-20100409-0045555
Source code file: toppush.c, line: 631

Fatal error:
Unknown bond_atomtype OSL

OSL is defined in the atomtypes.atp file located in the force field
folder that I constructed.  Thus, I do not understand why it is

Does anybody know how to address this error?

Many Thanks,
Peter Huwe

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